Connectomes.jl

This is the documentation for Connectomes.jl, a package made for working with human brain connectomes, simulating dynamical systems on networks and visualising brain related images.

Working with Connectomes

A Connectome is a spatially embedded graph $G = (V, E)$. The collection of vertices, $V$, are labelled nodes corresponding to discrete brain regions given by a particular brain parcellation, and the edge set, $E$, denotes edges between these vertices, as inferred from tractography.

Connectomes.jl comes with a connectome and parcellation. The file path can be found with the function:

using Connectomes

connectome_path = Connectomes.connectome_path()

"/home/runner/work/Connectomes.jl/Connectomes.jl/assets/connectomes/Connectomes-hcp-scale1.xml"

From this path, two datatypes can be loaded: a Parcellation or a Connectome. A parcellation underlies a connectome, so let's start with that. By default, we use the Desikan-Killiany-Tourville (DKT) atlas. A parcellation is simply a collection of Regions.

struct Parcellation
    regions::Vector{Region}
end

Where Regions comprise pertinent information relating to a given region.

struct Region
    ID::Int                 # DKT region ID number
    Label::String           # Region name
    Region::String          # Cortical or Subcortical
    Lobe::String            # Lobe the region belongs to
    Hemisphere::String      # Hemisphere the region belongs to
    x::Float64              # x coordinate 
    y::Float64              # y coordinate
    z::Float64              # z coordinate
end

The parcellation can be loaded from the connectome_path in the following way.

parc = Parcellation(connectome_path)

Parcellation with 83 regions

parc can be numerically indexed to retrieve regions, either as a Int

parc[1]

Region 1: right lateralorbitofrontal

or a Vector{Int}, which will return a new Parcellation.

parc[[1, 2, 3]]

Parcellation with 3 regions

If we load a Makie backend, we can conveniently plot the parcellation. Let's say, we just want to plot the left side of the connectome. We can do the following.

using WGLMakie

left_parc = filter(x -> get_lobe(x) == "subcortex", parc)

plot_parc(left_parc; resolution=(500, 350), view=:front)